3TMT

IrisFP, distorted chromophore


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.295 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The nature of transient dark States in a photoactivatable fluorescent protein.

Roy, A.Field, M.J.Adam, V.Bourgeois, D.

(2011) J.Am.Chem.Soc. 133: 18586-18589

  • DOI: 10.1021/ja2085355
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fluorescent proteins (FPs) of the green fluorescent protein family blink and bleach like all fluorophores. However, contrary to organic dyes, the mechanisms by which transient losses of fluorescence occur in FPs have received little attention. Here, ...

    Fluorescent proteins (FPs) of the green fluorescent protein family blink and bleach like all fluorophores. However, contrary to organic dyes, the mechanisms by which transient losses of fluorescence occur in FPs have received little attention. Here, we focus on the photoactivatable IrisFP, for which a transient non-fluorescent chromophoric state with distorted geometry was recently reported (Adam, V.; et al. J. Am. Chem. Soc. 009, 131, 18063). We investigated the chemical nature of this blinked state by employing quantum chemical/molecular mechanical calculations. Our findings suggest two previously unidentified dark states that display similar distorted chromophores with a transiently ruptured π-electron system. Both are protonated at atom C(α) of the chromophore methylene bridge. Transient protonation may occur via proton transfer from the nearby Arg66 either in the triplet state T(1) after intersystem crossing or in an anionic radical (doublet) ground state. As Arg66 is conserved in green-to-red photoconvertible FPs, these dark states are predicted to be common to all these proteins. We also suggest that C(α) protonated dark states may accelerate photobleaching by favoring decarboxylation of the fully conserved Glu212.


    Organizational Affiliation

    Institut de Biologie Structurale (IBS)-Jean-Pierre Ebel, CEA/CNRS/ Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green to red photoconvertible GPF-like protein EosFP
A, B, C, D
232Lobophyllia hemprichiiMutation(s): 2 
Find proteins for Q5S6Z9 (Lobophyllia hemprichii)
Go to UniProtKB:  Q5S6Z9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR8
Query on CR8
A, B, C, D
L-PEPTIDE LINKINGC17 H16 N5 O4HIS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.295 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.840α = 90.00
b = 96.510β = 90.00
c = 140.000γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
ADSCdata collection
PHASERphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-11-23
    Type: Structure summary
  • Version 1.2: 2011-11-30
    Type: Database references